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- EMDB-43928: Cryo-EM reconstruction of a catalytically active phospholipase c ... -

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Basic information

Entry
Database: EMDB / ID: EMD-43928
TitleCryo-EM reconstruction of a catalytically active phospholipase c epsilon
Map data
Sample
  • Complex: Cryo-EM reconstruction of a catalytically active PLCe
    • Protein or peptide: Phospholipase C epsilon
KeywordsGPCR signaling / complex / phospholipase / PIP2 hydrolysis / G proteins / MEMBRANE PROTEIN
Function / homology
Function and homology information


diacylglycerol biosynthetic process / Synthesis of IP3 and IP4 in the cytosol / phosphoinositide phospholipase C / phosphatidylinositol metabolic process / phospholipase C activity / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / glomerulus development / phosphatidylinositol-mediated signaling / lipid catabolic process / positive regulation of lamellipodium assembly ...diacylglycerol biosynthetic process / Synthesis of IP3 and IP4 in the cytosol / phosphoinositide phospholipase C / phosphatidylinositol metabolic process / phospholipase C activity / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / glomerulus development / phosphatidylinositol-mediated signaling / lipid catabolic process / positive regulation of lamellipodium assembly / release of sequestered calcium ion into cytosol / guanyl-nucleotide exchange factor activity / small GTPase binding / epidermal growth factor receptor signaling pathway / lamellipodium / phospholipase C-activating G protein-coupled receptor signaling pathway / Ras protein signal transduction / intracellular signal transduction / G protein-coupled receptor signaling pathway / Golgi membrane / enzyme binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1 / : / : / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain ...1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1 / : / : / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Phosphatidylinositol-specific phospholipase C, X domain / Phosphatidylinositol-specific phospholipase C, X domain / Phospholipase C, catalytic domain (part); domain X / Phosphatidylinositol-specific phospholipase X-box domain profile. / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / EF-hand domain pair / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.46 Å
AuthorsOhri V / Lyon AM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)1R01HL141076-01 United States
CitationJournal: To Be Published
Title: Cryo-EM reconstruction of a catalytically active Phospholipase C epsilon
Authors: Ohri V / Lyon AM
History
DepositionMar 5, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43928.png

Downloads & links

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Map

FileDownload / File: emd_43928.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 512 pix.
= 269.824 Å		0.53 Å/pix.
x 512 pix.
= 269.824 Å		0.53 Å/pix.
x 512 pix.
= 269.824 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.527 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.027045762 - 0.062123276
Average (Standard dev.)0.00026709147 (±0.0026012748)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 269.824 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43928_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43928_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43928_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM reconstruction of a catalytically active PLCe

EntireName: Cryo-EM reconstruction of a catalytically active PLCe
Components
  • Complex: Cryo-EM reconstruction of a catalytically active PLCe
    • Protein or peptide: Phospholipase C epsilon

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Supramolecule #1: Cryo-EM reconstruction of a catalytically active PLCe

SupramoleculeName: Cryo-EM reconstruction of a catalytically active PLCe / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Sample contained a mix of PLCe PH-COOH and RhoA-GTP. This reconstruction is from a volume class representing PLCe, but lacking the flexibly tethered PH domain.
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 165 KDa

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Macromolecule #1: Phospholipase C epsilon

MacromoleculeName: Phospholipase C epsilon / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HHHHHHSSGV DLGTENLYFQ SNADHGTELI PWYVLSIQAD VHQFLLQGAT VIHYDQDTHL SARCFLQLQP DNSTLTWMKP PTASPAGAR LKLGVLSNVA EPGKFPSLGN AGVSGLVEGI LDLFSVKAVY MGHPGIDIHT VCVQNKLSSM LLSETGVTLL Y GLQTTDNR ...String:
HHHHHHSSGV DLGTENLYFQ SNADHGTELI PWYVLSIQAD VHQFLLQGAT VIHYDQDTHL SARCFLQLQP DNSTLTWMKP PTASPAGAR LKLGVLSNVA EPGKFPSLGN AGVSGLVEGI LDLFSVKAVY MGHPGIDIHT VCVQNKLSSM LLSETGVTLL Y GLQTTDNR LLHFVAPKHT AKMLFSGLLE LTTAVRKIRK FPDQRQQWLR KQYVSFYQED GRYEGPTLAH AVELFGGRRW ST RNPSPGM SAKNAEKPNM QRNNTLGIST TKKKKKMLMR GESGEVTDDE MATRKAKMYR ECRSRSGSDP QEANEQEDSE ANV ITNPPN PLHSRRAYSL TTAGSPNLAT GMSSPISAWS SSSWHGRIKG GMKGFQSFMV SDSNMSFIEF VELFKSFSIR SRKD LKDIF DIYSVPCNRS ASESTPLYTN LTIEENTNDL QPDLDLLTRN VSDLGLFMKS KQQLSDNQRQ ISDAIAAASI VTNGT GIES TSLGIFGVGI LQLNDFLVNC QGEHCTYDEI LSIIQKFEPN ISMCHQGLLS FEGFARFLMD KDNFASKNDE SRENKK DLQ LPLSYYYIES SHNTYLTGHQ LKGESSVELY SQVLLQGCRS IELDCWDGDD GMPIIYHGHT LTTKIPFKEV VEAIDRS AF ITSDLPIIIS IENHCSLPQQ RKMAEIFKSV FGEKLVAKFL FETDFSDDPM LPSPDQLRRK VLLKNKKLKA HQTPVDIL K QKAHQLASMQ TQAFTGGNAN PPPASNEEEE DEEDEYDYDY ESLSDDNILE DRPENKSCAD KLQFEYNEEV PKRIKKADN SSGNKGKVYD MELGEEFYLP QNKKESRQIA PELSDLVIYC QAVKFPGLST LNSSGSGRGK ERKSRKSIFG NNPGRMSPGE TASFNRTSG KSSCEGIRQI WEEPPLSPNT SLSAIIRTPK CYHISSLNEN AAKRLCRRYS QKLIQHTACQ LLRTYPAATR I DSSNPNPL MFWLHGIQLV ALNYQTDDLP LHLNAAMFEA NGGCGYVLKP PVLWDKSCPM YQKFSPLERD LDAMDPATYS LT IISGQNV CPSNSTGSPC IEVDVLGMPL DSCHFRTKPI HRNTLNPMWN EQFLFRVHFE DLVFLRFAVV ENNSSAITAQ RII PLKALK RGYRHLQLRN LHNEILEISS LFINSRRMED NPSGSTRPAS LMFNTEERKC SQTHKVTVHG VPGPEPFAVF TINE GTKAK QLLQQILAVD QDTKLTAADY FLMEEKHFIS KEKNECRKQP FQRAVGPEED IVQILNSWFP EEGYVGRIVL KPQQE TLEE KNIVHDDREV ILSSEEESFF VQVHDVSPEQ PRTVIKAPRV STAQDVIQQT LCKAKYSYSI LNNPNPCDYV LLEEVM KDA PNKKSSTPKS SQRILLDQEC VFQAQSKWKG AGKFILKLKE QVQASREDKR RGISFASELK KLTKSTKQTR GLTSPPQ LV ASESVQSKEE KPMGALASGD TAGYQS

UniProtKB: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
150.0 mMNaClsodium chloride
2.0 mMDTTdithiothreitol
0.1 mMEDTAethylenediaminetetraacetic acid
0.1 mMEGTAegtazic acid
1.0 mMMgCl2magnesium dichloride
0.04 mMGTPguanosine triphosphate
0.5 mMCaCl2calcium chloride
2.5 mMCHAPS3-((3-cholamidopropyl) dimethylammonio)-1-propanesulfonate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6345 / Average exposure time: 3.2 sec. / Average electron dose: 57.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1329298
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104904
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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